To differentiate the skin-dwelling filariae Mansonella streptocerca and Onchocerca volvulus, a nested polymerase chain reaction (PCR) assay was developed from small amounts of parasite material present in skin biopsies. One nonspecific and one specific pair of primers were used to amplify the 5S rDNA spacer region of M. streptocerca. Biopsies with different microfilaria densities obtained from 104 Ugandans living in an area endemic for M. streptocerca were tested using both the nested PCR assay and standard parasitologic assessment of microfilariae. All 82 samples from microfilaria carriers were positive when tested using the nested PCR assay. In addition, M. streptocerca DNA could be detected in 16 samples thought to be microfilaria negative. Furthermore, six days following ivermectin treatment, M. streptocerca DNA was found in 12 of 14 microfilaria-negative biopsies. Control skin samples from patients infected with O. volvulus were all negative in the nested PCR assay. This assay improves the diagnosis of M. streptocerca and will facilitate further epidemiologic studies.